\name{compare.all.trees}
\alias{compare.all.trees}
\title{Compare all trees in a treeset, and return a matrix (lower diagonal only) indicating which pairwise comparisons are identical}
\description{Compare all trees in a treeset, and return a matrix (lower diagonal only) indicating which pairwise comparisons are identical}
\usage{
compare.all.trees(treeset, ...)
}
\arguments{
  \item{treeset}{an object of class \code{multiPhylo} or a list of \code{phylo} objects}
  \item{...}{additional arguments to be passed along to \code{all.equal.phylo}}
}
\details{Slow, tedious one-on-one comparison of trees, depending on the implementation in \code{ape}. 
         As written, this function is sensitive to rooting.}
\value{A matrix of \code{TRUE} and \code{FALSE} values depending on whether the compared trees are identical in topology}
\author{Andrew Hipp}
\seealso{
	\code{link{unique.multiPhylo}}
}
